PEAKS export for library building

PEAKS export for library building mauro galli  2019-09-26

I am a new user and I have a question about the Cut-off score setting in the library building for a DIA analysis.

I processed the data on PEAKS applying 1% FDR and I exported the file for Skyline. In the ion library building process in Skyline, I set the Cut-off score equal to 0, not to apply a double filter on my peptides (I don't want to cut 1% of the file where I already cut 1%). Do you think it could be a problem?

Thanks in advance!

Brian Pratt responded:  2019-09-26

Hi Mauro,

That's entirely appropriate - as you say, there is no need to filter if you are already satisfied with all the peptides being presented to Skyline.

Thanks for using the Skyline support board!

Brian Pratt